Merge pull request #577 from Open-Systems-Pharmacology/develop

Version 8.0.4

OSPSuite.Core.sln

@@ -30,6 +30,8 @@ Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "OSPSuite.Core.Tests", "test
 EndProject
 Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "OSPSuite.UI.Tests", "tests\OSPSuite.UI.Tests\OSPSuite.UI.Tests.csproj", "{A3DF5E6B-9EC5-4F19-9240-8050B23459B4}"
 EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "OSPSuite.Engine", "src\OSPSuite.Engine\OSPSuite.Engine.csproj", "{C08DB78D-D281-4F32-86D3-A38868BEF9D6}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -68,12 +70,17 @@ Global
 		{A3DF5E6B-9EC5-4F19-9240-8050B23459B4}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{A3DF5E6B-9EC5-4F19-9240-8050B23459B4}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{A3DF5E6B-9EC5-4F19-9240-8050B23459B4}.Release|Any CPU.Build.0 = Release|Any CPU
+		{C08DB78D-D281-4F32-86D3-A38868BEF9D6}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{C08DB78D-D281-4F32-86D3-A38868BEF9D6}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{C08DB78D-D281-4F32-86D3-A38868BEF9D6}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{C08DB78D-D281-4F32-86D3-A38868BEF9D6}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		VisualSVNWorkingCopyRoot = .
+		SolutionGuid = {49DFC778-454E-4009-BBCD-C5984EF0F2DE}
 	EndGlobalSection
 	GlobalSection(NDepend) = preSolution
 		Project = ".\OSPSuite.Core.ndproj"

SolutionInfo.cs

@@ -3,10 +3,10 @@
 using System.Runtime.InteropServices;
 [assembly: AssemblyCompany("Open Systems Pharmacology Community")]
 [assembly: AssemblyProduct("OSPSuite.Core")]
-[assembly: AssemblyCopyright("Copyright © 2017 - Open Systems Pharmacology Community")]
+[assembly: AssemblyCopyright("Copyright © 2002-2019 - Open Systems Pharmacology Community")]
 [assembly: ComVisible(false)]
-[assembly: AssemblyVersion("1.0.0.0")]
-[assembly: AssemblyFileVersion("1.0.0.0")]
+[assembly: AssemblyVersion("1.0.0")]
+[assembly: AssemblyFileVersion("1.0.0")]
 [assembly: AssemblyInformationalVersion("")]
 [assembly: InternalsVisibleTo("OSPSuite.Core.Tests")]
 [assembly: InternalsVisibleTo("OSPSuite.UI.Tests")]

appveyor-coverage.yml

@@ -2,7 +2,7 @@ configuration: Debug
 image: Visual Studio 2017
 
 environment:
-  app_version: '7.4.0'
+  app_version: '8.0'
 
 version: '$(app_version).{build}'
 
@@ -24,7 +24,7 @@ before_build:
   - nuget sources add -name databinding-devexpress -source https://ci.appveyor.com/nuget/ospsuite-databinding-devexpress 
   - nuget sources add -name funcparser -source https://ci.appveyor.com/nuget/ospsuite-funcparser 
   - nuget sources add -name simmodel -source https://ci.appveyor.com/nuget/ospsuite-simmodel
-  - nuget sources add -name cvodes -source https://ci.appveyor.com/nuget/ospsuite-simmodel-solver-cvodes-282
+  - nuget sources add -name cvodes -source https://ci.appveyor.com/nuget/ospsuite-simmodel-solver-cvodes
   - nuget sources add -name smartxls -source https://ci.appveyor.com/nuget/ospsuite-smartxls
   - nuget restore
 

appveyor.yml

@@ -2,7 +2,7 @@ configuration: Debug
 image: Visual Studio 2017
 
 environment:
-  app_version: '7.4.0'
+  app_version: '8.0'
 
 version: '$(app_version).{build}'
 
@@ -24,7 +24,7 @@ before_build:
   - nuget sources add -name databinding-devexpress -source https://ci.appveyor.com/nuget/ospsuite-databinding-devexpress 
   - nuget sources add -name funcparser -source https://ci.appveyor.com/nuget/ospsuite-funcparser 
   - nuget sources add -name simmodel -source https://ci.appveyor.com/nuget/ospsuite-simmodel
-  - nuget sources add -name cvodes -source https://ci.appveyor.com/nuget/ospsuite-simmodel-solver-cvodes-282
+  - nuget sources add -name cvodes -source https://ci.appveyor.com/nuget/ospsuite-simmodel-solver-cvodes
   - nuget sources add -name smartxls -source https://ci.appveyor.com/nuget/ospsuite-smartxls
   - nuget restore
 
@@ -41,8 +41,8 @@ branches:
     - develop
 test:
   assemblies:
-    - OSPSuite.Core.Tests.dll
-    - OSPSuite.UI.Tests.dll
+    - '**\OSPSuite.Core.Tests\bin\$(configuration)\OSPSuite.Core.Tests.dll'
+    - '**\OSPSuite.UI.Tests\bin\$(configuration)\OSPSuite.UI.Tests.dll'
 
 install:
  - git submodule update --init --recursive
@@ -62,4 +62,4 @@ nuget:
 notifications:
   - provider: Slack
     incoming_webhook:      
-      secure: 4MH9Em6TtrKalq6808dhPOqypTfYBJvVlqPaa9akNyF1h7st5qNdNezFp6T+bWXqrcZ4q/smtPcJ7LkUFHL46JDYUFlIL8FDz+ApX/vP+x0=
+      secure: 4MH9Em6TtrKalq6808dhPOqypTfYBJvVlqPaa9akNyFEAs8X080yIO8g1FLt3tNfBN4OpeBnkgrXzf7AqNKV5561x7Coux3ByGrHmsL1sCo=

rakefile.rb

@@ -6,6 +6,7 @@
   filter << "+[OSPSuite.Core]*"
   filter << "+[OSPSuite.Infrastructure]*"
   filter << "+[OSPSuite.Presentation]*"
+  filter << "+[OSPSuite.Engine]*"
 
   #exclude namespaces that are tested from applications
   filter << "-[OSPSuite.Infrastructure]OSPSuite.Infrastructure.Reporting*"

src/OSPSuite.Assets/OSPSuite.Assets.csproj

@@ -35,8 +35,8 @@
     <WarningLevel>4</WarningLevel>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="OSPSuite.Utility, Version=3.0.0.3, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\packages\OSPSuite.Utility.3.0.0.3\lib\net462\OSPSuite.Utility.dll</HintPath>
+    <Reference Include="OSPSuite.Utility, Version=3.0.1.7, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\OSPSuite.Utility.3.0.1.7\lib\net462\OSPSuite.Utility.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />

src/OSPSuite.Assets/UIConstants.cs

@@ -185,6 +185,9 @@ public static class Captions
       public static readonly string ValueOriginSource = "Source";
       public static readonly string ValueOriginDeterminationMethod = "Method";
       public static readonly string ValueOrigin = "Value Origin";
+      public static readonly string CalculationMethod = "Calculation Method";
+      public static readonly string MoleculeObserver = "Molecule Observer";
+      public static readonly string ContainerObserver = "Container Observer";
 
       public static string ShouldWatermarkBeUsedForChartExportToClipboard(string applicationName, string optionLocation)
       {
@@ -356,7 +359,7 @@ public static class Importer
          public class ToolTips
          {
             public static readonly string NamingPattern = "Set a pattern for renaming imported data";
-            public static readonly string RnageSelect = "Override the default range by selecting a new range and pressing OK.\nTo revert to the default range click OK without a new range selected.";
+            public static readonly string RangeSelect = "Override the default range by selecting a new range and pressing OK.\nTo revert to the default range click OK without a new range selected.";
          }
 
          public static readonly string ImportFileFilter = "Excel Files (*.xls, *.xlsx)|*.xls;*.xlsx|Comma Separated Value Files (*.csv)|*.csv|NonMem Files (*.NMdat)|*.NMdat|All Files (*.*)|*.*";
@@ -1108,8 +1111,8 @@ public static class Error
       public static readonly string JournalNotOpen = "Journal is not open";
       public static readonly string NoPagesToExport = "There are no pages to export";
       public static readonly string TemplateShouldContainAtLeastOneCurve = "Template should contain at least one curve.";
-      public static readonly string SessionFactoryNotInitalized = "Session factory is not initalized";
-      public static readonly string SessionNotInitalized = "Session not initialized";
+      public static readonly string SessionFactoryNotInitialized = "Session factory is not initialized";
+      public static readonly string SessionNotInitialized = "Session not initialized";
       public static readonly string SessionDisposed = "Session was disposed";
       public static readonly string OutputMappingHasInconsistentDimension = "Output mapping has inconsistent dimension";
       public static readonly string WeightValueCannotBeNegative = "Weights cannot be negative";
@@ -1183,10 +1186,9 @@ public static string SensitivityParameterIsInvalid(string name)
       public static readonly string CovarianceMatrixCannotBeCalculated = "Covariance matrix cannot be calculated";
       public static readonly string CorrelationMatrixCannotBeCalculated = "Correlation matrix cannot be calculated";
 
-      public static string CannotSelectTheSamePartialProcessMoreThanOnce(string name)
-      {
-         return $"'{name}' cannot be selected more than once.";
-      }
+      public static string CannotSelectTheSamePartialProcessMoreThanOnce(string name) => $"'{name}' cannot be selected more than once.";
+
+      public static string CannotSelectTheObservedDataMoreThanOnce(string name) => $"'{name}' cannot be selected more than once for the same output.";
 
       public static string DimensionMismatchError(IEnumerable<string> dimensionNames)
       {
@@ -1238,15 +1240,9 @@ public static string WrongColumnDimensions(string columnName, int xDim, int yDim
 
       public const string OnlyLocalParametersInPassiveTransports = "Passive transport {0} contains parameters with BuildMode != LOCAL";
 
-      public static string BothNeighborsSatisfying(string neighborhood)
-      {
-         return $"Both neighbors of {neighborhood} satisfy the criteria";
-      }
+      public static string BothNeighborsSatisfying(string neighborhood) => $"Both neighbors of {neighborhood} satisfy the criteria";
 
-      public static string BothNeighborsSatisfyingForTransport(string message, string transporter)
-      {
-         return $"{message} for transport {transporter}";
-      }
+      public static string BothNeighborsSatisfyingForTransport(string message, string transporter) => $"{message} for transport {transporter}";
 
       public static readonly string UnknownParameterBuildMode = "Unknown molecule parameter build mode";
       public static readonly string ConstMoleculeParameterInNeighborhood = "Constant parameters are not allowed in the molecule properties container of the neighborhood";
@@ -1271,10 +1267,10 @@ public static string UndefinedHelpParameter(string calculationMethod, string cat
 
       public static string UndefinedFormulaInHelpParameter(string parameterName, string calculationMethod, string category)
       {
-         return $"Cannot add help parmaeter '{parameterName}' with an undefined formula (null) in calculation method '{calculationMethod}' for category '{category}'";
+         return $"Cannot add help parameter '{parameterName}' with an undefined formula (null) in calculation method '{calculationMethod}' for category '{category}'";
       }
 
-      public static string TwoDiffentFormulaForSameParameter(string parameter, string parameterPath)
+      public static string TwoDifferentFormulaForSameParameter(string parameter, string parameterPath)
       {
          return $"Formula in parameter '{parameter}' with path '{parameterPath}' was described inconsistently by more than one calculation.";
       }
@@ -1362,8 +1358,18 @@ public static string LastDataRowLessThanFirstDataRow(int dataEndRow, int dataSta
          return $"Cannot import data from {sheetName} worksheet.{Environment.NewLine}The first data row index is greater than the last data row index";
       }
 
+      public static string ExportToCsvNotSupportedForDifferentBaseGrid = "Export to CSV is only supported for data columns sharing the same base grid.";
+
       public const string MESSAGE_ERROR_NAN = "Error information has been truncated because invalid values have been replaced by NaN.\n\n An arithmetic error must be at least 0.\n A geometric error must be at least 1.\n";
 
+      public const string QualificationOutputFolderNotDefined = "Qualification output folder not defined.";
+
+      public const string QualificationObservedDataFolderNotDefined = "Qualification observed data folder not defined.";
+
+      public const string QualificationMappingFileNotDefined = "Qualification mapping file not defined.";
+
+      public const string QualificationReportConfigurationFileNotDefined = "Qualification report configuration file not defined.";
+
 
       public static class SensitivityAnalysis
       {
@@ -1540,25 +1546,27 @@ public static class Parameters
          public static readonly string ValueShouldBeBetweenMinAndMax = "Value should be greater than minimum value and smaller than maximum value.";
          public static readonly string MinShouldBeStrictlyGreaterThanZeroForLogScale = "Minimum value should be greater than zero or the scaling should be set to linear.";
 
-         public static string MinimumMustBeGreaterThanOrEqualTo(double minValue, string fullQuantityPath)
+         public static string MinimumMustBeGreaterThanOrEqualTo(string minDisplayValue, string displayUnit, string fullQuantityPath)
          {
-            return $"The minimum value must be greater than or equal to {minValue} for parameter '{fullQuantityPath}";
+            return $"The minimum value must be greater than or equal to {valueWithUnit(minDisplayValue,displayUnit)} for parameter '{fullQuantityPath}'";
          }
 
-         public static string MinimumMustBeGreaterThan(double minValue, string fullQuantityPath)
+         public static string MinimumMustBeGreaterThan(string minDisplayValue, string displayUnit, string fullQuantityPath)
          {
-            return $"The minimum value must be greater than {minValue} for parameter '{fullQuantityPath}'";
+            return $"The minimum value must be greater than {valueWithUnit(minDisplayValue, displayUnit)} for parameter '{fullQuantityPath}'";
          }
 
-         public static string MaximumMustBeLessThanOrEqualTo(double maxValue, string fullQuantityPath)
+         public static string MaximumMustBeLessThanOrEqualTo(string maxDisplayValue, string displayUnit, string fullQuantityPath)
          {
-            return $"The maximum value must be less than or equal to {maxValue} for parameter '{fullQuantityPath}";
+            return $"The maximum value must be less than or equal to {valueWithUnit(maxDisplayValue, displayUnit)} for parameter '{fullQuantityPath}'";
          }
 
-         public static string MaximumMustBeLessThan(double maxValue, string fullQuantityPath)
+         public static string MaximumMustBeLessThan(string maxDisplayValue, string displayUnit, string fullQuantityPath)
          {
-            return $"The maximum value must be less than {maxValue} for parameter '{fullQuantityPath}";
+            return $"The maximum value must be less than {valueWithUnit(maxDisplayValue, displayUnit)} for parameter '{fullQuantityPath}'";
          }
+
+         private static string valueWithUnit(string value, string unit) => string.IsNullOrEmpty(unit) ? value : $"{value} {unit}";
       }
    }
 
@@ -1571,7 +1579,7 @@ public static class Warning
    {
       public static readonly string OptimizedValueIsCloseToBoundary = "Identified value is close to boundary";
       public static readonly string ImportingParameterIdentificationValuesFromCancelledRun = "This parameter identification run was cancelled.\nDo you really want to import the identified parameters?";
-      public static readonly string ImportingParameterIdentificationValuesFromCategorialRun = "Only the VALUES of the identified parameters will be transfered.\nPlease set the calculation methods manually.";
+      public static readonly string ImportingParameterIdentificationValuesFromCategorialRun = "Only the VALUES of the identified parameters will be transferred.\nPlease set the calculation methods manually.";
       public static readonly string CurveNameIsMissing = "Curve name is missing";
    }
 
@@ -1735,9 +1743,9 @@ public static class Command
 
       public static string CreateProjectDescription(string version) => $"Project started with version {version}";
 
-      public static string SetMetaDataAddedCommandDescripton(string name, string value) => $"New Meta Data added where {name} = {value}";
+      public static string SetMetaDataAddedCommandDescription(string name, string value) => $"New Meta Data added where {name} = {value}";
 
-      public static string SetMetaDataRemovedCommandDescripton(string name, string value) => $"Meta Data removed where {name} = {value}";
+      public static string SetMetaDataRemovedCommandDescription(string name, string value) => $"Meta Data removed where {name} = {value}";
 
       public static string SetMetaDataChangedCommandDescription(string oldName, string oldValue, string newName, string newValue)
       {

src/OSPSuite.Assets/packages.config

@@ -1,4 +1,4 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
-  <package id="OSPSuite.Utility" version="3.0.0.3" targetFramework="net462" />
+  <package id="OSPSuite.Utility" version="3.0.1.7" targetFramework="net462" />
 </packages>

src/OSPSuite.Core/Chart/ChartUpdate.cs

@@ -7,18 +7,18 @@ public class ChartUpdate : IDisposable
    {
       private readonly IEventPublisher _eventPublisher;
       private readonly IChart _chart;
-      private readonly bool _propogateChartChangeEvent;
+      private readonly bool _propagateChartChangeEvent;
 
-      public ChartUpdate(IEventPublisher eventPublisher, IChart chart, bool propogateChartChangeEvent)
+      public ChartUpdate(IEventPublisher eventPublisher, IChart chart, bool propagateChartChangeEvent)
       {
          _eventPublisher = eventPublisher;
          _chart = chart;
-         _propogateChartChangeEvent = propogateChartChangeEvent;
+         _propagateChartChangeEvent = propagateChartChangeEvent;
       }
 
       public void Dispose()
       {
-         _eventPublisher.PublishEvent(new ChartUpdatedEvent(_chart,_propogateChartChangeEvent));
+         _eventPublisher.PublishEvent(new ChartUpdatedEvent(_chart,_propagateChartChangeEvent));
       }
    }
 }

src/OSPSuite.Core/Chart/ChartUpdater.cs

@@ -4,7 +4,7 @@ namespace OSPSuite.Core.Chart
 {
    public interface IChartUpdater
    {
-      ChartUpdate UpdateTransaction(IChart chart, bool propogateChartChangeEvent =true);
+      ChartUpdate UpdateTransaction(IChart chart, bool propagateChartChangeEvent =true);
       void Update(IChart chart);
    }
 
@@ -17,9 +17,9 @@ public ChartUpdater(IEventPublisher eventPublisher)
          _eventPublisher = eventPublisher;
       }
 
-      public ChartUpdate UpdateTransaction(IChart chart, bool propogateChartChangeEvent = true)
+      public ChartUpdate UpdateTransaction(IChart chart, bool propagateChartChangeEvent = true)
       {
-         return new ChartUpdate(_eventPublisher, chart, propogateChartChangeEvent);
+         return new ChartUpdate(_eventPublisher, chart, propagateChartChangeEvent);
       }
 
       public void Update(IChart chart)

src/OSPSuite.Core/Chart/CurveChart.cs

@@ -261,10 +261,9 @@ public void RemoveCurvesForColumn(DataColumn dataColumn)
          removeCurves(curve => curve.xData == dataColumn || curve.yData == dataColumn);
       }
 
-      public void RemoveCurvesForDataRepository(DataRepository dataRepository)
-      {
-         removeCurves(curve => dataRepository.Contains(curve.xData.Id) || dataRepository.Contains(curve.yData.Id));
-      }
+      public void RemoveCurvesForColumns(IEnumerable<DataColumn> dataColumns) => dataColumns.Each(RemoveCurvesForColumn);
+
+      public void RemoveCurvesForDataRepository(DataRepository dataRepository) => RemoveCurvesForColumns(dataRepository);
 
       private void removeCurves(Func<Curve, bool> shouldRemoveCurveFunc)
       {

src/OSPSuite.Core/Chart/Events.cs

@@ -12,11 +12,11 @@ protected ChartEvent(IChart chart)
 
    public class ChartUpdatedEvent : ChartEvent
    {
-      public bool PropogateChartChangeEvent { get; }
+      public bool PropagateChartChangeEvent { get; }
 
-      public ChartUpdatedEvent(IChart chart, bool propogateChartChangeEvent) : base(chart)
+      public ChartUpdatedEvent(IChart chart, bool propagateChartChangeEvent) : base(chart)
       {
-         PropogateChartChangeEvent = propogateChartChangeEvent;
+         PropagateChartChangeEvent = propagateChartChangeEvent;
       }
    }
 

src/OSPSuite.Core/Commands/AddObservedDataMetaDataCommand.cs

@@ -20,7 +20,7 @@ protected override void ExecuteWith(IOSPSuiteExecutionContext context)
       {
          setMetaDataInRepository();
 
-         Description = Command.SetMetaDataAddedCommandDescripton(_metaDataKeyValue.Key, _metaDataKeyValue.Value);
+         Description = Command.SetMetaDataAddedCommandDescription(_metaDataKeyValue.Key, _metaDataKeyValue.Value);
          SetBuildingBlockParameters(context);
          context.PublishEvent(new ObservedDataMetaDataAddedEvent(_observedData));
       }